ENST00000904792.1:c.-1507G>A

Variant names:

• chr13-111319384-G-A
• rs2479967
• ENST00000904792.1:c.-1507G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000904792.1(TEX29):​c.-1507G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,058 control chromosomes in the GnomAD database, including 6,853 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6853 hom., cov: 32)
• Consequence: TEX29 ENST00000904792.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613
• Publications: 6 publications found

Genes affected

TEX29 (HGNC:20370): (testis expressed 29) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC105370365 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000904792.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX29	NM_001303133.1		c.-110-1473G>A		intron	N/A	NP_001290062.1	Q8N6K0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX29	ENST00000904792.1		c.-1507G>A		5_prime_UTR	Exon 1 of 5	ENSP00000574851.1
	TEX29	ENST00000497241.5	TSL:5	n.48-1473G>A		intron	N/A	ENSP00000431661.1	F2Z350

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42465 AN: 151940 Hom.: 6845 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.267

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.280 AC: 42502 AN: 152058 Hom.: 6853 Cov.: 32 AF XY: 0.287 AC XY: 21353 AN XY: 74342

African (AFR) AF: 0.253 AC: 10490 AN: 41464

American (AMR) AF: 0.360 AC: 5502 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3468

East Asian (EAS) AF: 0.816 AC: 4215 AN: 5166

South Asian (SAS) AF: 0.347 AC: 1667 AN: 4810

European-Finnish (FIN) AF: 0.282 AC: 2983 AN: 10582

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16247 AN: 67970

Other (OTH) AF: 0.273 AC: 576 AN: 2108

Alfa AF: 0.272 Hom.: 1173

Bravo AF: 0.289

Asia WGS AF: 0.559 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.71
PhyloP100		0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2479967;

hg19: chr13-111971731;